Mathematician/statistician developing network methods for the analysis of multi-omics data

Before IMforFUTURE: background
I come from Omis, a small coastal town in Croatia. From an early age, I enjoyed solving mathematical problems and riddles, so I decided to go to the gymnasium with a mathematical program. I continued this path and got my bachelor’s (2014) and master’s degree (2016) in mathematics at the University of Split, Croatia. However, during my studies, I discovered the love for probability and statistics and was fascinated by various applications of mathematics. I was lucky to attend the Research MIMOmics Summer School in Cambridge in the summer of 2017 where I started to learn about statistics in omics. After that and while reading more and more about omics research, I was sure that I wanted to work with modelling and analyzing different omics datasets.
IMforFUTURE fellowship
In November 2017 I started my fellowship at the University of Bologna as one of 11 IMforFUTURE’s Early Stage Researchers. In Bologna, I work at the Department of Physics and Astronomy where I collaborate with the group of biophysicists including my supervisor Prof. Gastone Castellani. We work daily on various omics data trying to model and understand the biological processes.
Evolutionary models of omics data
While the importance of Gaussian normal distribution can’t be disputed, in biology we are often dealing with the other type of distribution: long-tailed distribution. Descriptively, long-tailed distribution is characterised by a large number of occurrences far from the centre of the distribution. Besides omics data, this distribution is found in population studies and as a degree distribution of real-life networks. Its omnipresence suggests that there are certain evolutionary mechanisms from which it emerges. This problem is well-studied in population dynamics and different stochastic models were developed to describe the processes leading to observed long-tailed distributions. We used a similar approach to model the dynamics of gene length and of protein domains. In both cases, we successfully explained the observed distributions and used the model parameters to describe the data.
Methylation network
Cytosine methylation in the humane genome is an important and well-studied epigenetic mark which has the potential to regulate gene expression. Since the process of methylation predominantly occurs at CG dinucleotide sequences, the target of studies are these so-called CpG sites. One of the available tools, Infinium 450k assay measures the level of methylation of ~450,000 CpG sites spread across the genome. Even though there are general rules in which CpG methylation or the lack of it regulates the expression of genes, there are many exceptions and we are far from understanding the exact regulatory mechanisms. The main problem is the group behaviour of CpG sites guided by their complicated correlated structure. We want to get a better understanding of this behaviour in order to successfully analyze the methylation data. To do so, we use network methods to model the methylation correlation structure.
Perks of being an IMforFUTURE fellow
Secondments
As part of being an IMforFUTURE Early Stage Researcher, we spend some periods with other partners. Besides collaboration with our fellow ESRs, we also get an interdisciplinary and intersectoral experience.
This way, I had an opportunity to spend 1 month at glyXera in Magdeburg, Germany. It was an amazing experience where my host Frania Zúñiga showed me how the work in lab and data production look like. Being mathematician/statistician, this offered me another perspective where I could finally see data as more than just numbers.
I also spent 3 months at the University of Leeds, UK. This secondment was a period I spent in the research group of my second supervisor Prof. Jeanine Houwing-Duistermaat and with my other colleague Maarten van Schaik. I participated in their weekly meetings and I got many nice suggestions about my research. There were also a lot of conferences/workshops I attended during my period in Leeds like LASR 2019 conference in Leeds and 7th Channel Network Conference in Rothamsted.
At my department in Bologna, we hosted two other fellows: Maarten van Schaik and Zhujie Gu. It was a nice period where we managed to discuss our research and plan collaborations.

Public engagement
All Early Stage Researchers take part in public engagement activities organised in their countries, such as European Researcher’s Night. Beyond that, we managed to organise a group public engagement activities in Split, Croatia. The activities lasted for three days and we shared our research with different generations: from school children to the general public who was strolling in the historic centre of Split. I helped with the organisation of Scientific Workshop for children where I designed games to present the networks in an entertaining way. I was amazed by the enthusiasm the children showed and by the ease with which they understood everything my colleagues and I presented. I also spent time talking to the general public about my research. Talking to stranger proved to be easier than I expected and we also managed to meet some fellow researchers on their vacation.
